1 Initial data visualisation

##       GC112 GC116 GC191
## Gnai3  2151  1396  1057
## Pbsn      0     0     0
## Cdc45  1422   560   581
## [1] 53546    36
## 
##    Chow Glucose Sucrose 
##      16      13       7
##    Sample    Diet
## 28  GC112 Glucose
## 29  GC116 Glucose
## 30  GC191 Glucose
## 31  GC195 Glucose
## 32  GC196 Glucose
## 33  GC197 Glucose
## 34  GC201 Glucose
## 35  GC202 Glucose
## 36  GC204 Glucose
## 37  GC206 Glucose
## 18  GC222 Sucrose
## 19  GC226 Sucrose
## 20  GC229 Sucrose
## 38   SL11 Glucose
## 23  SL114 Sucrose
## 1   SL142    Chow
## 2   SL145    Chow
## 39   SL15 Glucose
## 40   SL19 Glucose
## 8   SL221    Chow
## 9   SL223    Chow
## 10  SL225    Chow
## 12  SL227    Chow
## 7  SL2310    Chow
## 3   SL233    Chow
## 4   SL237    Chow
## 5   SL238    Chow
## 6   SL239    Chow
## 13  SL241    Chow
## 14  SL242    Chow
## 15  SL243    Chow
## 16  SL244    Chow
## 17  SL245    Chow
## 21   SL32 Sucrose
## 26   SL43 Sucrose
## 27   SL44 Sucrose
## 
##   FALSE 
## 1927656

## 
## FALSE  TRUE 
## 31078 22468
## [1] 20872    36

2 DE analysis & GSEA

  • databased: reactome for mice
  • using gage (wilcoxin-rank-sum test, null: assume most of them are not expressed)

2.1 Glucose vs Chow

2.2 Sucrose Vs Chow

2.3 Sucrose Vs Glucose